fixed a very strange bug in the goldstandard analyzer

de.uniwue.mk.athen/bundles/de.uniwue.mk.kall.athen.appDelegation/ressources/corefViewConfig.xml

+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<nappiPipelineConfiguration>
+    <engines>
+        <configurationParams>
+            <entry>
+                <key>PARAM_MODEL_LOCATION</key>
+                <value xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">http://ki.informatik.uni-wuerzburg.de/nappi/nappiOnlineRepository/models/openNLP/sentence/de-sent.bin</value>
+            </entry>
+        </configurationParams>
+        <engineClass>OpenNLPSentenceSplitter</engineClass>
+        <reader>false</reader>
+    </engines>
+    <engines>
+        <configurationParams>
+            <entry>
+                <key>PARAM_MODEL_LOCATION</key>
+                <value xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">http://ki.informatik.uni-wuerzburg.de/nappi/nappiOnlineRepository/models/openNLP/token/de-token.bin</value>
+            </entry>
+        </configurationParams>
+        <engineClass>OpenNLPTokenizer</engineClass>
+        <reader>false</reader>
+    </engines>
+    <engines>
+        <configurationParams>
+            <entry>
+                <key>PARAM_EXECUTABLE_LOCATION</key>
+                <value xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">http://ki.informatik.uni-wuerzburg.de/nappi/nappiOnlineRepository/executables/treetagger/bin/tree-tagger.exe</value>
+            </entry>
+            <entry>
+                <key>PARAM_MODEL_LOCATION</key>
+                <value xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">http://ki.informatik.uni-wuerzburg.de/nappi/nappiOnlineRepository/models/treetagger/pos/german-utf8.par</value>
+            </entry>
+        </configurationParams>
+        <engineClass>TreeTaggerLemmatizer</engineClass>
+        <reader>false</reader>
+    </engines>
+    <engines>
+        <configurationParams>
+            <entry>
+                <key>PARAM_EXECUTABLE_LOCATION</key>
+                <value xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">http://ki.informatik.uni-wuerzburg.de/nappi/nappiOnlineRepository/executables/treetagger/bin/tree-tagger.exe</value>
+            </entry>
+            <entry>
+                <key>PARAM_MODEL_LOCATION</key>
+                <value xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">http://ki.informatik.uni-wuerzburg.de/nappi/nappiOnlineRepository/models/treetagger/pos/german-utf8.par</value>
+            </entry>
+        </configurationParams>
+        <engineClass>TreeTaggerPOSTagger</engineClass>
+        <reader>false</reader>
+    </engines>
+    <engines>
+        <configurationParams>
+            <entry>
+                <key>PARAM_MODEL_LOCATION</key>
+                <value xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">http://ki.informatik.uni-wuerzburg.de/nappi/nappiOnlineRepository/models/rft/german-pc-64bit-utf8.par</value>
+            </entry>
+        </configurationParams>
+        <engineClass>RFTTagger</engineClass>
+        <reader>false</reader>
+    </engines>
+    <engines>
+        <configurationParams>
+            <entry>
+                <key>PARAM_MODEL_LOCATION</key>
+                <value xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">http://ki.informatik.uni-wuerzburg.de/nappi/nappiOnlineRepository/models/kallimachos/DROCTagger/nerAllModel.bin</value>
+            </entry>
+        </configurationParams>
+        <engineClass>DROCTagger</engineClass>
+        <reader>false</reader>
+    </engines>
+</nappiPipelineConfiguration>

de.uniwue.mk.athen/bundles/de.uniwue.mk.kall.athen.goldstandardAnalyzer/src/de/uniwue/mk/kall/athen/goldstandardAnalyzer/GoldstandardAnalyzer.java

@@ -49,44 +49,44 @@ import de.uniwue.mk.kall.athen.part.editor.annotations.UIMAInfo.VariableType;
 import de.uniwue.mk.kall.athen.part.editor.subordinate.AEditorSubordinateViewPart;
 
 public class GoldstandardAnalyzer extends AEditorSubordinateViewPart {
-	
+
 	private static final String TP = "de.uniwue.kalimachos.coref.type.TP";
 	private static final String FP = "de.uniwue.kalimachos.coref.type.FP";
 	private static final String FN = "de.uniwue.kalimachos.coref.type.FN";
 
 	// the reference to the UI
 	private GoldstandardAnalyzerWidget widget;
-		
+
 	// the mappings
 	List<GoldMappingConfig> mappings;
 	private Type currentSystemType;
 
 	private List<NAryTupel> content;
-	
+
 	private StyleRange styleRange;
-	
-	private Map <AnnotationFS, String> m = new HashMap<AnnotationFS, String>();
-	private Map <AnnotationFS, String> fpMap = new HashMap <AnnotationFS, String>();
-	private Map <AnnotationFS, String> fnMap = new HashMap<AnnotationFS, String>();
-	private Map <AnnotationFS, String> tpMap = new HashMap<AnnotationFS, String>();
 
-	private GoldstandardAnalyzerDrawingStrategy goldstandardAnalyzerDrawingStrategy = new GoldstandardAnalyzerDrawingStrategy(styleRange, m);
+	private Map<AnnotationFS, String> m = new HashMap<AnnotationFS, String>();
+	private Map<AnnotationFS, String> fpMap = new HashMap<AnnotationFS, String>();
+	private Map<AnnotationFS, String> fnMap = new HashMap<AnnotationFS, String>();
+	private Map<AnnotationFS, String> tpMap = new HashMap<AnnotationFS, String>();
+
+	private GoldstandardAnalyzerDrawingStrategy goldstandardAnalyzerDrawingStrategy = new GoldstandardAnalyzerDrawingStrategy(
+			styleRange, m);
 
-	
 	// UIMA Types, everything here will be injected by the annotation processor
 	@ATHENEditorDrawingInfo(mode = true, layer = 3)
 	@UIMAInfo(variableType = VariableType.TYPE, nameOrKey = TP)
 	private Type tpType;
-	
+
 	@ATHENEditorDrawingInfo(mode = true, layer = 2)
 	@UIMAInfo(variableType = VariableType.TYPE, nameOrKey = FP)
 	private Type fpType;
-	
+
 	@ATHENEditorDrawingInfo(mode = true, layer = 1)
 	@UIMAInfo(variableType = VariableType.TYPE, nameOrKey = FN)
 	private Type fnType;
 
-	private List<AnnotationFS> annoList;
+	// private List<AnnotationFS> annoList;
 
 	@PostConstruct
 	public void postConstruct(Composite parent, MPart part) {
@@ -214,49 +214,47 @@ public class GoldstandardAnalyzer extends AEditorSubordinateViewPart {
 
 	@Override
 	public boolean initTypes() {
-		
-		annoList = new ArrayList<AnnotationFS>();
-			
+
 		// process the annotations on the fields
-		AnnotationProcessor.processUIMAInfoAnnotations(this, editor.getCas());	
-		
+		AnnotationProcessor.processUIMAInfoAnnotations(this, editor.getCas());
+
 		// set everything unneeded invisible - editor should only display what
 		// is needed in this view
 		this.editor.allStylesInvisible();
-			
+
 		// layer
 		editor.changeLayer(tpType, 3);
 		editor.changeLayer(fpType, 2);
 		editor.changeLayer(fnType, 1);
-		
-		//true positive yellowgreen
+
+		// true positive yellowgreen
 		StyleRange rangeOv = new StyleRange();
-		rangeOv.background = new Color(Display.getCurrent(), 154,205,50);
+		rangeOv.background = new Color(Display.getCurrent(), 154, 205, 50);
 		AnnoStyle tpStyle = new AnnoStyle(new GoldstandardAnalyzerDrawingStrategy(rangeOv, m), rangeOv);
-		
+
 		editor.changeStyle(tpType, tpStyle);
 		editor.changeVisibility(tpType, true);
 		editor.setActiveMode(tpType);
-		
-		
-		//false positive firebrick
+
+		// false positive firebrick
 		StyleRange rangeOv1 = new StyleRange();
-		rangeOv1.background = new Color(Display.getCurrent(), 178,34,34);
+		rangeOv1.background = new Color(Display.getCurrent(), 178, 34, 34);
 		AnnoStyle fpStyle = new AnnoStyle(new GoldstandardAnalyzerDrawingStrategy(rangeOv1, m), rangeOv1);
-		
+
 		editor.changeStyle(fpType, fpStyle);
 		editor.changeVisibility(fpType, true);
 		editor.setActiveMode(fpType);
-		
-		//false negative firebrick
+
+		// false negative firebrick
 		StyleRange rangeOv2 = new StyleRange();
-		rangeOv2.background = new Color(Display.getCurrent(), 178,34,34);
-		AnnoStyle fnStyle = new AnnoStyle(new GoldstandardAnalyzerDrawingStrategy(rangeOv2, m), rangeOv2);;
-		
+		rangeOv2.background = new Color(Display.getCurrent(), 178, 34, 34);
+		AnnoStyle fnStyle = new AnnoStyle(new GoldstandardAnalyzerDrawingStrategy(rangeOv2, m), rangeOv2);
+		;
+
 		editor.changeStyle(fnType, fnStyle);
 		editor.changeVisibility(fnType, true);
 		editor.setActiveMode(fnType);
-		
+
 		return false;
 	}
 
@@ -290,35 +288,34 @@ public class GoldstandardAnalyzer extends AEditorSubordinateViewPart {
 		}
 
 	}
-	
+
 	private void deleteAnnotations(AnnotationFS... annos) {
 		List<AnnotationFS> toDelete = new ArrayList<>();
-		
+
 		toDelete.addAll(Arrays.asList(annos));
-		
+
 		editor.removeAnnotations(toDelete);
-		
-		for (AnnotationFS anno : toDelete)
-		{
+
+		for (AnnotationFS anno : toDelete) {
 			editor.getCas().removeFsFromIndexes(anno);
 		}
 	}
-	
-	
-	public void deleteAnnotations(List<AnnotationFS> annoList) {	
-		
+
+	public void deleteAnnotations() {
+
+		List<AnnotationFS> annoList = new ArrayList<>();
 		AnnotationIndex<AnnotationFS> annotationIndex = editor.getCas().getAnnotationIndex(tpType);
 		FSIterator<AnnotationFS> iterator = annotationIndex.iterator();
 		while (iterator.hasNext()) {
 			annoList.add((AnnotationFS) iterator.next());
 		}
-		
+
 		AnnotationIndex<AnnotationFS> annotationIndex1 = editor.getCas().getAnnotationIndex(fpType);
 		FSIterator<AnnotationFS> iterator1 = annotationIndex1.iterator();
 		while (iterator1.hasNext()) {
 			annoList.add((AnnotationFS) iterator1.next());
 		}
-		
+
 		AnnotationIndex<AnnotationFS> annotationIndex2 = editor.getCas().getAnnotationIndex(fnType);
 		FSIterator<AnnotationFS> iterator2 = annotationIndex2.iterator();
 		while (iterator2.hasNext()) {
@@ -326,11 +323,11 @@ public class GoldstandardAnalyzer extends AEditorSubordinateViewPart {
 		}
 		deleteAnnotations(annoList.toArray(new AnnotationFS[0]));
 	}
-	
+
 	public void compareTypes() {
-		
-		deleteAnnotations(annoList);
-		
+
+		deleteAnnotations();
+
 		content = mappingsToContent(mappings);
 		widget.refresh(content);
 		if (!content.isEmpty()) {
@@ -342,50 +339,51 @@ public class GoldstandardAnalyzer extends AEditorSubordinateViewPart {
 			EvaluationStruct evalStruct = calculateEvalStruct(content);
 			widget.updateScores(evalStruct);
 		}
-			
-		for (NAryTupel tupel : content){
-			if (tupel.getElementAt(0) == null){
+
+		for (NAryTupel tupel : content) {
+			if (tupel.getElementAt(0) == null) {
 				createFalsePositive(tupel);
 			}
-			
-			else if (tupel.getElementAt(0) != null){
+
+			else if (tupel.getElementAt(0) != null) {
 				createFalseNegativeOrTruePositive(tupel);
 			}
 		}
 	}
-	
-	public void createFalsePositive(NAryTupel t){
-		for (int k = 1; k < t.getTupelDimension(); k++){
-			if (t.getElementAt(k) != null){
-				AnnotationFS fpAnnotation = editor.getCas().createAnnotation(fpType, t.getElementAt(k).getBegin(), t.getElementAt(k).getEnd());
-				//annoList.add(fpAnnotation);
+
+	public void createFalsePositive(NAryTupel t) {
+		for (int k = 1; k < t.getTupelDimension(); k++) {
+			if (t.getElementAt(k) != null) {
+				AnnotationFS fpAnnotation = editor.getCas().createAnnotation(fpType, t.getElementAt(k).getBegin(),
+						t.getElementAt(k).getEnd());
+				// annoList.add(fpAnnotation);
 				String s = "Annotator" + k;
 				fpMap.put(fpAnnotation, s);
 			}
 		}
 		createMap();
 	}
-	
-	public void createFalseNegativeOrTruePositive(NAryTupel t){
+
+	public void createFalseNegativeOrTruePositive(NAryTupel t) {
 		int counter = 0;
-		for (int l = 1; l < t.getTupelDimension(); l++){
-			if (t.getElementAt(l) != null){
+		for (int l = 1; l < t.getTupelDimension(); l++) {
+			if (t.getElementAt(l) != null) {
 				counter++;
-			} 
-		}	
-		if (counter == t.getTupelDimension()-1){
-			createTruePositive(t);
+			}
 		}
-		else{
+		if (counter == t.getTupelDimension() - 1) {
+			createTruePositive(t);
+		} else {
 			createFalseNegative(t);
 		}
 	}
-	
-	public void createFalseNegative(NAryTupel t){
-		for (int k = 0; k < t.getTupelDimension(); k++){
-			if (t.getElementAt(k) != null){
-				AnnotationFS fnAnnotation = editor.getCas().createAnnotation(fnType, t.getElementAt(k).getBegin(), t.getElementAt(k).getEnd());
-				//annoList.add(fnAnnotation);
+
+	public void createFalseNegative(NAryTupel t) {
+		for (int k = 0; k < t.getTupelDimension(); k++) {
+			if (t.getElementAt(k) != null) {
+				AnnotationFS fnAnnotation = editor.getCas().createAnnotation(fnType, t.getElementAt(k).getBegin(),
+						t.getElementAt(k).getEnd());
+				// annoList.add(fnAnnotation);
 				String s = "Annotator" + k;
 				fnMap.put(fnAnnotation, s);
 			}
@@ -393,26 +391,28 @@ public class GoldstandardAnalyzer extends AEditorSubordinateViewPart {
 		createMap();
 	}
 
-	
-	public void createTruePositive(NAryTupel t){
-		AnnotationFS tpAnnotation = editor.getCas().createAnnotation(tpType, t.getElementAt(0).getBegin(), t.getElementAt(0).getEnd());
-		//annoList.add(tpAnnotation);
+	public void createTruePositive(NAryTupel t) {
+		AnnotationFS tpAnnotation = editor.getCas().createAnnotation(tpType, t.getElementAt(0).getBegin(),
+				t.getElementAt(0).getEnd());
+		// annoList.add(tpAnnotation);
 		String s = "Annotator" + "tp";
 		tpMap.put(tpAnnotation, s);
 		createMap();
 	}
-	
-	
-	public void createMap()
-	{
+
+	public void createMap() {
 		m.putAll(tpMap);
 		m.putAll(fpMap);
 		m.putAll(fnMap);
-		
+
 		goldstandardAnalyzerDrawingStrategy.updateAnnotations(m);
-		
+
 		for (AnnotationFS anno : m.keySet()) {
-			editor.getCas().addFsToIndexes(anno);
+			if (anno != null || !(anno instanceof AnnotationFS)) {
+				editor.getCas().addFsToIndexes(anno);
+			} else {
+				System.out.println("How can this even happen! A null annotation!");
+			}
 		}
 		editor.updateWidget();
 	}

de.uniwue.mk.athen/bundles/de.uniwue.mk.kall.athen.goldstandardAnalyzer/src/de/uniwue/mk/kall/athen/goldstandardAnalyzer/struct/NAryTupel.java

@@ -65,6 +65,7 @@ public class NAryTupel implements Iterable<AnnotationFS> {
 	public void insert(AnnotationFS anno) {
 
 		if (anno != null) {
+			//TODO this cannot deal with comparisons of the same type
 			Integer integer = typeToIndexMap.get(anno.getType());
 			tupelEntries.set(integer, anno);
 		}

de.uniwue.mk.athen/bundles/de.uniwue.mk.kall.athen.goldstandardAnalyzer/src/de/uniwue/mk/kall/athen/goldstandardAnalyzer/ui/GoldstandardAnalyzerDrawingStrategy.java

@@ -53,6 +53,9 @@ public class GoldstandardAnalyzerDrawingStrategy implements IAnnotationDrawingSt
 		if (m.containsKey(anno));
 		{
 			annotator = m.get(anno);
+			if(annotator==null){
+				return;
+			}
 			if (annotator.equals("Annotatortp")){
 				gc.setBackground(yellowgreen);				
 			} else if (annotator.equals("Annotator0")){

de.uniwue.mk.athen/bundles/de.uniwue.mk.kall.athen.goldstandardAnalyzer/src/de/uniwue/mk/kall/athen/goldstandardAnalyzer/util/AnnotationComparisonUtil.java

@@ -43,6 +43,8 @@ public class AnnotationComparisonUtil {
 		/*
 		 * Check Gold Annotations
 		 */
+		System.out.println(goldList.size());
+		System.out.println(systemRemaining.size());
 		goldList.forEach(goldAnno -> {
 			AnnotationFS foundAnno = null;
 			for (AnnotationFS systemAnno : systemRemaining) {

de.uniwue.mk.athen/bundles/de.uniwue.mk.kall.athen.goldstandardAnalyzer/src/de/uniwue/mk/kall/athen/goldstandardAnalyzer/widgets/GoldStandardTreeTableComposite.java

@@ -112,6 +112,8 @@ public class GoldStandardTreeTableComposite extends Composite {
 
 	public void refresh(List<NAryTupel> content) {
 
+		if (content == null)
+			return;
 		createTreeTable(content);
 
 		addTreeTableSelectionListener();